Using RNA-seq (Mortazavi et al., 2008), high-resolution
genome-wide maps of the mouse transcriptome in various mouse (C57BL/6)
tissues, primary cells, cell lines of different developmental stage and age groups were generated.
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Cells were grown according to the approved
ENCODE cell culture protocols.
RNA samples from tissues and primary cells were extracted
from Trizol® according to protocol (Invitrogen). Long PolyA+ RNA
was purified with the Dynabeads mRNA purification kit (Invitrogen).
The mRNA libraries were prepared for strand-specific sequencing as
described previously (Parkhomchuk et al., 2009).
Sequencing and Analysis
Samples were sequenced on Illumina Genome Analyzer II,
Genome Analyzer IIx and HiSeq 2000 platforms
for 36 cycles. Image analysis, base calling and
alignment to the mouse genome version NCBI37/mm9 were performed
using Illumina's RTA.
Alignment to the mouse genome was performed using
TopHat (Trapnell et al., 2009). Wig files were
generated by TopHat and expression levels were
calculated with Cufflinks (Trapnell et al., 2010).
This is Release 2 (Mar 2012). It contains a total of 22 RNA-seq experiments with the addition of 12 new experiments.
These data were generated and analyzed in
Bing Ren's laboratory
at the Ludwig Institute for Cancer Research.
Contact: Yin Shen
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Nat Methods. 2008 Jul;5(7):621-8.
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A.
Transcriptome analysis by strand-specific sequencing of complementary DNA.
Nucleic Acids Res. 2009 Oct;37(18):e123.
PMID: 19620212; PMC: PMC2764448
Trapnell C, Pachter L, Salzberg SL.
TopHat: discovering splice junctions with RNA-Seq.
Bioinformatics. 2009 May 1;25(9):1105-11.
PMID: 19289445; PMC: PMC2672628
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform
switching during cell differentiation.
Nat Biotechnol. 2010 May;28(5):511-5.
PMID: 20436464; PMC: PMC3146043
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